Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory Xinyu Gua,b, Nicholas P. Schafera,b,c, Qian Wanga, Sarah S. Songd, Mingchen Chena, M. Neal Waxhamd, and Peter G. Wolynesa,b,1 aCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005; bDepartment of Chemistry, Rice University, Houston, TX 77005; cSchafer Science, LLC, Houston, TX 77025; and dDepartment of Neurobiology and Anatomy, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030 Contributed by Peter G. Wolynes, July 21, 2020 (sent for review June 29, 2020; reviewed by Angel E. Garcia and J. Andrew McCammon) Dendritic spines are tiny membranous protrusions on the den- by Stephan et al. (5)] and then to model its structure in complex drites of neurons. Dendritic spines change shape in response to with F-actin. input signals, thereby strengthening the connections between Actin cytoskeleton remodeling is involved in the structural neurons. The growth and stabilization of dendritic spines is change of dendritic spines, which is associated with the strength- thought to be essential for maintaining long-term memory. Actin ening of synapses and, therefore, also with the storage of memories cytoskeleton remodeling in spines is a key element of their forma- (11, 12). Stephan et al. (5) observed that CPEB3 aggregates tion and growth. More speculatively, the aggregation of CPEB3, a colocalize with F-actin in neurons and that the depolymerization of functional prion that binds RNA, has been reported to be involved F-actin prevents CPEB3 from aggregating in yeast. In previously in the maintenance of long-term memory. Here we study the in- published theoretical work (13) on the CPEB3 homolog from teraction between actin and CPEB3 and propose a molecular Aplysia (ApCPEB), it was suggested that the CPEB/F-actin inter- model for the complex structure of CPEB3 and an actin filament action could provide the mechanical force necessary to induce a (F-actin). The results of our computational modeling, including structural transition of CPEB oligomers from a coiled-coil form both energetic and structural analyses, are compared with novel into a beta-sheet–containing amyloid-like fiber. Moreover, actin data from peptide array experiments. Our model of the CPEB3/ mRNA has been identified as a target of CPEB3, implying then F-actin interaction suggests that F-actin potentially triggers the that there may exist a positive feedback loop involving CPEB3 and aggregation-prone structural transition of a short CPEB3 sequence F-actin (5) wherein F-actin facilitates the aggregation of CPEB3 BIOPHYSICS AND COMPUTATIONAL BIOLOGY by zipping it into a beta-hairpin form. We also propose that the and then CPEB3 aggregates promote the translation of actin, ul- CPEB3/F-actin interaction might be regulated by the SUMOylation timately influencing spine structure. of CPEB3, based on bioinformatic searches for potential SUMOyla- In this study, we present a structure of the F-actin/CPEB3- tion sites as well as SUMO interacting motifs in CPEB3. On the ABD complex found through computational modeling using the basis of these results and the existing literature, we put forward RaptorX complex contact prediction webserver in concert with a possible molecular mechanism underlying long-term memory the Associative Memory, Water-Mediated, Structure and Energy that involves CPEB3’s binding to actin, its aggregation, and its Model with Evolutionary Restraints (AWSEM-ER) (14, 15). regulation by SUMOylation. AWSEM-ER is a coarse-grained force field that has been opti- mized using energy landscape theory which can be bolstered by long-term memory | functional prion | dendritic spine Significance tructural change of dendritic spines is associated with the – Sformation and maintenance of long-term memory (1 3). A The growth and stabilization of dendritic spines is thought to synaptic tag is required to mark growing spines and regulate local be essential for strengthening the connections between neu- translation of synaptic proteins there. Rapid biomolecular turn- rons and thereby memories. Actin cytoskeleton remodeling in over (4), however, raises the question of how synaptic structural spines is the basis of this growth and stabilization. A functional change is maintained so as to be long-lasting. The mammalian cy- prion that binds mRNA, CPEB3, which interacts with actin, has toplasmic polyadenylation element-binding protein 3 (CPEB3), a been reported to be involved in the maintenance of long-term functional prion that binds to RNA (5), is involved in long-term memory by forming stable aggregates. Here we study the in- potentiation (LTP) and has emerged as a potentially important teraction between actin and CPEB3 and propose a molecular factor in the persistence of long-term memory. Homologs of model for the complex structure of CPEB3 bound to an actin CPEB3 in invertebrates, ApCPEB in Aplysia (6, 7) and Orb2 in filament. Our model gives insights into the actin/CPEB3 posi- Drosophila (8), have also been described as functional prions that tive feedback loop underlying long-term memory which in- regulate local protein synthesis in active synapses by binding to volves CPEB3’s binding to actin, its aggregation, and its RNA. Similarly, in higher organisms, CPEB3, with its proline- and regulation by SUMOylation. glutamine-rich (P/Q-rich) N-terminal prion domain (PRD) and C-terminal RNA binding domain (RBD), can form stable aggre- Author contributions: X.G., N.P.S., Q.W., S.S.S., M.C., M.N.W., and P.G.W. designed re- gates that are thought to consolidate synaptic strength and regulate search; X.G., N.P.S., S.S.S., M.C., and M.N.W. performed research; X.G., N.P.S., Q.W., S.S.S., M.C., M.N.W., and P.G.W. contributed new reagents/analytic tools; X.G., N.P.S., the local translation of target mRNAs upon synaptic stimulation Q.W., S.S.S., M.C., M.N.W., and P.G.W. analyzed data; and X.G., N.P.S., M.N.W., and (5). Numerous structural and cellular experiments on proteins in P.G.W. wrote the paper. the CPEB family have been performed. The Cryo-EM structure of Reviewers: A.E.G., Los Alamos National Laboratory; and J.A.M., University of California, Orb2 amyloid core (9) and the NMR structure of the CPEB RBD San Diego. (10) have been solved. The structures and functions of the re- Competing interest statement: N.P.S. is the founder of Schafer Science, LLC. mainder of CPEB3, including the structures of monomeric and Published under the PNAS license. amyloid PRD as well as the mechanism by which it aggregates, are 1To whom correspondence may be addressed. Email: [email protected]. still unknown. Here we combine bioinformatics studies, molecular This article contains supporting information online at https://www.pnas.org/lookup/suppl/ simulations, and peptide array experiments to refine the boundaries doi:10.1073/pnas.2012964117/-/DCSupplemental. of an Actin Binding Domain (ABD) in CPEB3 [initially identified www.pnas.org/cgi/doi/10.1073/pnas.2012964117 PNAS Latest Articles | 1of7 Downloaded by guest on September 27, 2021 predicted contacts, in this case from the RaptorX webserver. Integrating structure prediction and energetic analyses with ex- perimental peptide array data, we conclude that electrostatic interactions are essential to the stability of the bound complex and that a hydrophobic interaction cooperates with the electro- statics to guide the CPEB3-ABD to a binding pocket on the surface of F-actin. This binding pocket is shared by most other actin binding proteins, such as cofilin and Arp 2/3 (16). By clustering the F-actin/CPEB3-ABD complex structures from the simulation, we found a chameleon sequence in the N-terminal end of the ABD, which can adopt two different sec- ondary structures. When CPEB3 approaches the surface of actin, the electrostatic attraction between F-actin and the two ends of this chameleon sequence facilitates the formation of a beta-hairpin. This beta-hairpin acts as a catalyst for forming intramolecular beta- sheets and could thereby help trigger the aggregation of CPEB3. Actin-induced beta-sheet formation in CPEB3, however, pre- sents a potential problem if aggregation were unregulated inside neurons. SUMOylation is known to regulate CPEB3 aggregation (17), and we propose that this reversible posttranslational modification may be an important control to the CPEB3/F-actin Fig. 1. CPEB3 subdomain definitions and experimental peptide array data interaction. We performed bioinformatic searches for both showing per-residue actin binding intensity to peptides derived from the SUMOylation sites as well as SUMO interacting motifs in sequence of human CPEB3. (A) Definitions of CPEB3 subdomains used by CPEB3 and found several of both including a SUMO interacting Stephan et al. (5) (Upper) and in this work (Lower). (B) Experimental residue- motif in a region of CPEB3 that is crucial for binding to actin in level actin-binding intensity along the sequence of human CPEB3. The dashed blue lines enclose the ABD identified in this work (Q164 to T325). our predicted complex structure. We propose that SUMOylation of CPEB3 in its basal state might repress the CPEB3/F-actin interaction and that deSUMOylation in stimulated synapses then experiments by Stephan et al. (5) show that F-actin is required disinhibits this interaction so that the binding, aggregation, and for foci formation of a truncated mouse CPEB3 construct made regulatory activity of CPEB3 can be controlled ultimately by up of PRD2 and RBD, while foci formation for the RBD alone synaptic stimulation. This hypothesis is consistent with the ex- was not obviously influenced by F-actin depolymerization (5). perimental observations of Drisaldi et al. (17). As a bridge be- This result suggests that at least part of PRD2 interacts with tween synaptic stimulation and CPEB3 aggregation/activation, F-actin.